The coastal area of Niterói is marked by intensive naval activities and holds one of the countries main naval estates. The harbour and dockyards have been sited in the international literature as potential sources and sinks for accumulation of heavy metals and hence contaminated sediments. The aim of this paper is to assess the concentrations of heavy metals in Niterói Harbour and verify their bioavailability by determining the catalytic effects of the bacteria using esterase activity (EST) and electron transport system activity (ETSA). Samples were analysed for Ni, Zn, Pb, Cr and Cu and normalisation procedures were used to assess whether their concentrations represent background or contamination of the sediment. Heavy metal concentrations, especially for Cu, Zn and Pb were found to be much higher than natural background levels and the index of “geoaccumulation” shows moderate to extreme contamination. However, the absence of the inhibition of dehydrogenase activity indicated that the analysed heavy metals are not bioavailable in the EC50 values.